sampleReads: Sampling sequence read positions from a read density.
In ChIPsim: Simulation of ChIP-seq experiments

Description Usage Arguments Details Value Author(s) See Also Examples

Given a read density this function returns the starting positions of sequence reads.

1	sampleReads(readDens, nreads = 6e+06, strandProb = c(0.5, 0.5))

`readDens`	A two column matrix of read densities (as produced by `bindDens2readDens`).
`nreads`	Number of read positions to generate.
`strandProb`	A numeric vector with two elements giving weights for forward and reverse strand.

The expected number of reads for each strand is strandProb * nreads.

A list with components fwd and rev giving the read positions on the forward and reverse strand respectively.

Peter Humburg

bindDens2readDens

set.seed(1)
## generate a (relatively short) sequence of nucleosome features
features <- placeFeatures(start=200, length=1e5)

## calculate feature density
featureDens <- feat2dens(features, length=1e5)

## convert to read density
readDens <- bindDens2readDens(featureDens, fragDens, meanLength=160) 

## sample reads
## of course you would usually want a much larger number
readPos <- sampleReads(readDens, nreads=1000)